Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 3 19:06:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6z_15893/07_2023/8b6z_15893.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6z_15893/07_2023/8b6z_15893.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6z_15893/07_2023/8b6z_15893.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6z_15893/07_2023/8b6z_15893.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6z_15893/07_2023/8b6z_15893.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b6z_15893/07_2023/8b6z_15893.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 8 5.49 5 S 16 5.16 5 C 2240 2.51 5 N 624 2.21 5 O 693 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 3581 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3406 Number of conformers: 1 Conformer: "" Number of residues, atoms: 442, 3406 Classifications: {'peptide': 442} Link IDs: {'PCIS': 2, 'PTRANS': 24, 'TRANS': 415} Chain: "B" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 175 Classifications: {'RNA': 8} Modifications used: {'rna3p_pur': 6, 'rna3p_pyr': 2} Link IDs: {'rna3p': 7} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLY A 50 " occ=0.00 ... (2 atoms not shown) pdb=" O GLY A 50 " occ=0.00 Time building chain proxies: 2.63, per 1000 atoms: 0.73 Number of scatterers: 3581 At special positions: 0 Unit cell: (65.934, 93.906, 67.932, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 P 8 15.00 O 693 8.00 N 624 7.00 C 2240 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 667.4 milliseconds 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 806 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 5 sheets defined 25.1% alpha, 33.3% beta 1 base pairs and 4 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'A' and resid 19 through 32 Processing helix chain 'A' and resid 35 through 50 Processing helix chain 'A' and resid 57 through 66 Processing helix chain 'A' and resid 97 through 105 Processing helix chain 'A' and resid 121 through 127 removed outlier: 3.703A pdb=" N ILE A 127 " --> pdb=" O PHE A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 144 Processing helix chain 'A' and resid 154 through 158 removed outlier: 3.836A pdb=" N SER A 157 " --> pdb=" O LYS A 154 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N THR A 158 " --> pdb=" O MET A 155 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 154 through 158' Processing helix chain 'A' and resid 163 through 182 removed outlier: 3.601A pdb=" N TYR A 177 " --> pdb=" O GLU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 188 Processing helix chain 'A' and resid 227 through 234 removed outlier: 3.715A pdb=" N ALA A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 418 through 421 Processing sheet with id=AA1, first strand: chain 'A' and resid 79 through 81 removed outlier: 6.557A pdb=" N ILE A 8 " --> pdb=" O THR A 88 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE A 90 " --> pdb=" O ILE A 8 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N ILE A 10 " --> pdb=" O ILE A 90 " (cutoff:3.500A) removed outlier: 8.782A pdb=" N CYS A 111 " --> pdb=" O HIS A 7 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ASN A 9 " --> pdb=" O CYS A 111 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N VAL A 113 " --> pdb=" O ASN A 9 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N VAL A 11 " --> pdb=" O VAL A 113 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE A 115 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 7.084A pdb=" N ILE A 13 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ALA A 117 " --> pdb=" O ILE A 13 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A 191 " --> pdb=" O VAL A 150 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 214 through 216 Processing sheet with id=AA3, first strand: chain 'A' and resid 247 through 249 removed outlier: 6.659A pdb=" N ASN A 311 " --> pdb=" O LYS A 290 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N VAL A 292 " --> pdb=" O GLY A 309 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLY A 309 " --> pdb=" O VAL A 292 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N MET A 294 " --> pdb=" O ASN A 307 " (cutoff:3.500A) removed outlier: 9.275A pdb=" N ASN A 307 " --> pdb=" O MET A 294 " (cutoff:3.500A) removed outlier: 4.478A pdb=" N THR A 261 " --> pdb=" O VAL A 312 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 247 through 249 Processing sheet with id=AA5, first strand: chain 'A' and resid 386 through 389 removed outlier: 6.610A pdb=" N ALA A 373 " --> pdb=" O VAL A 405 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N VAL A 405 " --> pdb=" O ALA A 373 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N LEU A 375 " --> pdb=" O GLU A 403 " (cutoff:3.500A) removed outlier: 7.207A pdb=" N GLU A 403 " --> pdb=" O LEU A 375 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N ALA A 338 " --> pdb=" O PRO A 406 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN A 339 " --> pdb=" O GLU A 442 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N GLN A 343 " --> pdb=" O ILE A 438 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N ILE A 438 " --> pdb=" O GLN A 343 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N ILE A 345 " --> pdb=" O GLY A 436 " (cutoff:3.500A) removed outlier: 5.617A pdb=" N GLY A 436 " --> pdb=" O ILE A 345 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N THR A 432 " --> pdb=" O ASP A 428 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ASP A 428 " --> pdb=" O THR A 432 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N VAL A 360 " --> pdb=" O ARG A 427 " (cutoff:3.500A) 136 hydrogen bonds defined for protein. 366 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2 hydrogen bonds 4 hydrogen bond angles 0 basepair planarities 1 basepair parallelities 4 stacking parallelities Total time for adding SS restraints: 1.10 Time building geometry restraints manager: 1.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1126 1.34 - 1.46: 522 1.46 - 1.57: 1984 1.57 - 1.69: 15 1.69 - 1.81: 26 Bond restraints: 3673 Sorted by residual: bond pdb=" C ILE A 235 " pdb=" N LEU A 236 " ideal model delta sigma weight residual 1.327 1.339 -0.012 1.39e-02 5.18e+03 7.88e-01 bond pdb=" N VAL A 152 " pdb=" CA VAL A 152 " ideal model delta sigma weight residual 1.465 1.476 -0.011 1.38e-02 5.25e+03 5.94e-01 bond pdb=" CA GLY A 351 " pdb=" C GLY A 351 " ideal model delta sigma weight residual 1.514 1.505 0.010 1.41e-02 5.03e+03 4.55e-01 bond pdb=" CA HIS A 364 " pdb=" CB HIS A 364 " ideal model delta sigma weight residual 1.530 1.541 -0.011 1.69e-02 3.50e+03 4.23e-01 bond pdb=" C LYS A 165 " pdb=" O LYS A 165 " ideal model delta sigma weight residual 1.236 1.228 0.008 1.26e-02 6.30e+03 4.09e-01 ... (remaining 3668 not shown) Histogram of bond angle deviations from ideal: 100.40 - 107.13: 190 107.13 - 113.87: 2104 113.87 - 120.61: 1326 120.61 - 127.34: 1322 127.34 - 134.08: 66 Bond angle restraints: 5008 Sorted by residual: angle pdb=" N GLY A 182 " pdb=" CA GLY A 182 " pdb=" C GLY A 182 " ideal model delta sigma weight residual 113.18 120.51 -7.33 2.37e+00 1.78e-01 9.56e+00 angle pdb=" N SER A 157 " pdb=" CA SER A 157 " pdb=" C SER A 157 " ideal model delta sigma weight residual 112.88 115.26 -2.38 1.29e+00 6.01e-01 3.40e+00 angle pdb=" CB LYS A 172 " pdb=" CG LYS A 172 " pdb=" CD LYS A 172 " ideal model delta sigma weight residual 111.30 115.15 -3.85 2.30e+00 1.89e-01 2.80e+00 angle pdb=" CA GLY A 182 " pdb=" C GLY A 182 " pdb=" N TYR A 183 " ideal model delta sigma weight residual 116.69 119.99 -3.30 2.04e+00 2.40e-01 2.62e+00 angle pdb=" N ASN A 200 " pdb=" CA ASN A 200 " pdb=" CB ASN A 200 " ideal model delta sigma weight residual 113.15 110.58 2.57 1.63e+00 3.76e-01 2.48e+00 ... (remaining 5003 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.78: 2053 13.78 - 27.56: 106 27.56 - 41.33: 33 41.33 - 55.11: 14 55.11 - 68.89: 4 Dihedral angle restraints: 2210 sinusoidal: 951 harmonic: 1259 Sorted by residual: dihedral pdb=" CA VAL A 152 " pdb=" C VAL A 152 " pdb=" N ASN A 153 " pdb=" CA ASN A 153 " ideal model delta harmonic sigma weight residual -180.00 -161.01 -18.99 0 5.00e+00 4.00e-02 1.44e+01 dihedral pdb=" CA PRO A 160 " pdb=" C PRO A 160 " pdb=" N ALA A 161 " pdb=" CA ALA A 161 " ideal model delta harmonic sigma weight residual -180.00 -162.08 -17.92 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA ILE A 178 " pdb=" C ILE A 178 " pdb=" N LYS A 179 " pdb=" CA LYS A 179 " ideal model delta harmonic sigma weight residual 180.00 162.10 17.90 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 2207 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 309 0.025 - 0.050: 155 0.050 - 0.075: 37 0.075 - 0.100: 31 0.100 - 0.125: 37 Chirality restraints: 569 Sorted by residual: chirality pdb=" CA ILE A 401 " pdb=" N ILE A 401 " pdb=" C ILE A 401 " pdb=" CB ILE A 401 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.93e-01 chirality pdb=" CA VAL A 405 " pdb=" N VAL A 405 " pdb=" C VAL A 405 " pdb=" CB VAL A 405 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.84e-01 chirality pdb=" CA VAL A 292 " pdb=" N VAL A 292 " pdb=" C VAL A 292 " pdb=" CB VAL A 292 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 ... (remaining 566 not shown) Planarity restraints: 613 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 419 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO A 420 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 420 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 420 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 418 " -0.021 5.00e-02 4.00e+02 3.26e-02 1.70e+00 pdb=" N PRO A 419 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 419 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 419 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 358 " 0.016 5.00e-02 4.00e+02 2.43e-02 9.41e-01 pdb=" N PRO A 359 " -0.042 5.00e-02 4.00e+02 pdb=" CA PRO A 359 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 359 " 0.013 5.00e-02 4.00e+02 ... (remaining 610 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 924 2.81 - 3.33: 3215 3.33 - 3.85: 5926 3.85 - 4.38: 6908 4.38 - 4.90: 11870 Nonbonded interactions: 28843 Sorted by model distance: nonbonded pdb=" OD2 ASP A 74 " pdb=" OG SER A 76 " model vdw 2.286 2.440 nonbonded pdb=" O ALA A 231 " pdb=" OG1 THR A 234 " model vdw 2.388 2.440 nonbonded pdb=" O VAL A 277 " pdb=" OG SER A 329 " model vdw 2.390 2.440 nonbonded pdb=" OH TYR A 29 " pdb=" NE1 TRP A 58 " model vdw 2.391 2.520 nonbonded pdb=" OE2 GLU A 68 " pdb=" N ARG A 96 " model vdw 2.413 2.520 ... (remaining 28838 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.70 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 24.230 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 15.660 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5668 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.023 3673 Z= 0.146 Angle : 0.507 7.329 5008 Z= 0.273 Chirality : 0.044 0.125 569 Planarity : 0.004 0.041 613 Dihedral : 10.482 68.887 1404 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 0.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.37), residues: 440 helix: -0.07 (0.48), residues: 93 sheet: -0.11 (0.60), residues: 83 loop : -0.67 (0.35), residues: 264 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 0.394 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 70 average time/residue: 1.3580 time to fit residues: 97.6490 Evaluate side-chains 32 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 32 time to evaluate : 0.385 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 37 optimal weight: 50.0000 chunk 33 optimal weight: 30.0000 chunk 18 optimal weight: 0.8980 chunk 11 optimal weight: 50.0000 chunk 22 optimal weight: 50.0000 chunk 17 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 13 optimal weight: 50.0000 chunk 20 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 39 optimal weight: 30.0000 overall best weight: 6.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 251 GLN A 311 ASN A 349 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5862 moved from start: 0.3048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 3673 Z= 0.215 Angle : 0.696 13.166 5008 Z= 0.350 Chirality : 0.048 0.153 569 Planarity : 0.005 0.041 613 Dihedral : 7.607 56.757 564 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.39), residues: 440 helix: 0.65 (0.53), residues: 95 sheet: -0.09 (0.52), residues: 100 loop : -0.58 (0.38), residues: 245 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 29 time to evaluate : 0.450 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 35 average time/residue: 1.6629 time to fit residues: 60.0443 Evaluate side-chains 23 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 21 time to evaluate : 0.406 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.5446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 22 optimal weight: 50.0000 chunk 12 optimal weight: 9.9990 chunk 33 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 11 optimal weight: 0.8980 chunk 40 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 35 optimal weight: 10.0000 chunk 39 optimal weight: 8.9990 chunk 13 optimal weight: 50.0000 chunk 32 optimal weight: 10.0000 overall best weight: 7.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5910 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 3673 Z= 0.224 Angle : 0.669 14.293 5008 Z= 0.338 Chirality : 0.046 0.141 569 Planarity : 0.005 0.049 613 Dihedral : 7.620 53.065 564 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.38), residues: 440 helix: 0.52 (0.51), residues: 95 sheet: 0.19 (0.54), residues: 95 loop : -0.61 (0.36), residues: 250 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 22 time to evaluate : 0.423 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 1 residues processed: 27 average time/residue: 1.3835 time to fit residues: 38.7967 Evaluate side-chains 21 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.389 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.5166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 39 optimal weight: 50.0000 chunk 30 optimal weight: 8.9990 chunk 20 optimal weight: 9.9990 chunk 4 optimal weight: 50.0000 chunk 19 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 chunk 40 optimal weight: 40.0000 chunk 42 optimal weight: 8.9990 chunk 38 optimal weight: 0.8980 chunk 11 optimal weight: 50.0000 chunk 35 optimal weight: 6.9990 overall best weight: 7.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5946 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.046 3673 Z= 0.207 Angle : 0.621 9.212 5008 Z= 0.313 Chirality : 0.045 0.138 569 Planarity : 0.005 0.054 613 Dihedral : 7.549 57.596 564 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 2.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.37), residues: 440 helix: 0.52 (0.51), residues: 97 sheet: -0.20 (0.54), residues: 90 loop : -0.81 (0.35), residues: 253 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 21 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 27 average time/residue: 1.2324 time to fit residues: 34.7661 Evaluate side-chains 21 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 18 time to evaluate : 0.449 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.1656 time to fit residues: 0.7753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 40.0000 chunk 0 optimal weight: 70.0000 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 36 optimal weight: 30.0000 chunk 29 optimal weight: 4.9990 chunk 21 optimal weight: 8.9990 chunk 38 optimal weight: 0.3980 chunk 10 optimal weight: 8.9990 chunk 14 optimal weight: 50.0000 chunk 8 optimal weight: 30.0000 overall best weight: 4.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN A 339 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5938 moved from start: 0.4648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 3673 Z= 0.163 Angle : 0.592 9.424 5008 Z= 0.295 Chirality : 0.045 0.139 569 Planarity : 0.005 0.055 613 Dihedral : 7.397 58.990 564 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.37), residues: 440 helix: 0.73 (0.51), residues: 97 sheet: 0.27 (0.53), residues: 97 loop : -0.62 (0.35), residues: 246 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 26 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 20 time to evaluate : 0.465 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 0 residues processed: 25 average time/residue: 1.0764 time to fit residues: 28.4088 Evaluate side-chains 18 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 18 time to evaluate : 0.442 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 50.0000 chunk 10 optimal weight: 0.0050 chunk 42 optimal weight: 20.0000 chunk 35 optimal weight: 20.0000 chunk 19 optimal weight: 50.0000 chunk 3 optimal weight: 40.0000 chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 50.0000 chunk 41 optimal weight: 7.9990 chunk 4 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 overall best weight: 4.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5949 moved from start: 0.4988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 3673 Z= 0.161 Angle : 0.590 9.125 5008 Z= 0.292 Chirality : 0.045 0.137 569 Planarity : 0.005 0.056 613 Dihedral : 7.252 55.783 564 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.38), residues: 440 helix: 0.93 (0.52), residues: 97 sheet: 0.47 (0.55), residues: 95 loop : -0.60 (0.35), residues: 248 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 19 time to evaluate : 0.362 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 2 residues processed: 25 average time/residue: 1.1697 time to fit residues: 30.6432 Evaluate side-chains 20 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 18 time to evaluate : 0.454 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.5986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 24 optimal weight: 0.8980 chunk 35 optimal weight: 50.0000 chunk 23 optimal weight: 20.0000 chunk 42 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 12 optimal weight: 20.0000 chunk 8 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5953 moved from start: 0.5277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.032 3673 Z= 0.155 Angle : 0.557 8.541 5008 Z= 0.281 Chirality : 0.044 0.135 569 Planarity : 0.005 0.058 613 Dihedral : 7.145 54.996 564 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 1.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.38), residues: 440 helix: 1.08 (0.53), residues: 97 sheet: 0.42 (0.55), residues: 95 loop : -0.62 (0.35), residues: 248 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 19 time to evaluate : 0.434 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 21 average time/residue: 1.1202 time to fit residues: 24.8705 Evaluate side-chains 22 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 19 time to evaluate : 0.436 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.1913 time to fit residues: 0.7983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 20 optimal weight: 0.0570 chunk 3 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 38 optimal weight: 0.2980 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 chunk 23 optimal weight: 3.9990 chunk 17 optimal weight: 30.0000 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 overall best weight: 1.2702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5910 moved from start: 0.5385 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 3673 Z= 0.134 Angle : 0.554 10.375 5008 Z= 0.275 Chirality : 0.044 0.134 569 Planarity : 0.005 0.056 613 Dihedral : 6.699 58.093 564 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.73 % Favored : 97.27 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.38), residues: 440 helix: 1.12 (0.52), residues: 97 sheet: 0.48 (0.55), residues: 95 loop : -0.57 (0.36), residues: 248 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 19 time to evaluate : 0.403 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 22 average time/residue: 1.0286 time to fit residues: 23.9355 Evaluate side-chains 20 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 19 time to evaluate : 0.433 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.5692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 35 optimal weight: 10.0000 chunk 37 optimal weight: 50.0000 chunk 39 optimal weight: 7.9990 chunk 25 optimal weight: 30.0000 chunk 41 optimal weight: 9.9990 chunk 19 optimal weight: 30.0000 chunk 29 optimal weight: 0.8980 chunk 43 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 3 optimal weight: 10.0000 overall best weight: 6.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5972 moved from start: 0.5635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 3673 Z= 0.183 Angle : 0.586 10.556 5008 Z= 0.289 Chirality : 0.044 0.133 569 Planarity : 0.006 0.061 613 Dihedral : 6.578 52.507 564 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 1.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.38), residues: 440 helix: 1.20 (0.53), residues: 97 sheet: 0.35 (0.53), residues: 98 loop : -0.60 (0.36), residues: 245 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 19 time to evaluate : 0.413 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 22 average time/residue: 1.0715 time to fit residues: 24.9142 Evaluate side-chains 21 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.451 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.5935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 26 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 37 optimal weight: 50.0000 chunk 10 optimal weight: 50.0000 chunk 32 optimal weight: 0.3980 chunk 5 optimal weight: 50.0000 chunk 9 optimal weight: 10.0000 chunk 34 optimal weight: 30.0000 chunk 14 optimal weight: 50.0000 chunk 35 optimal weight: 7.9990 overall best weight: 6.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5969 moved from start: 0.5811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 3673 Z= 0.179 Angle : 0.588 12.468 5008 Z= 0.293 Chirality : 0.045 0.135 569 Planarity : 0.005 0.060 613 Dihedral : 6.661 54.340 564 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 0.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.38), residues: 440 helix: 1.14 (0.53), residues: 97 sheet: 0.40 (0.52), residues: 100 loop : -0.56 (0.37), residues: 243 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 880 Ramachandran restraints generated. 440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 19 time to evaluate : 0.429 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 21 average time/residue: 1.0174 time to fit residues: 22.7379 Evaluate side-chains 20 residues out of total 373 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 18 time to evaluate : 0.436 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 1 average time/residue: 0.0912 time to fit residues: 0.7025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 44 random chunks: chunk 4 optimal weight: 30.0000 chunk 6 optimal weight: 30.0000 chunk 30 optimal weight: 30.0000 chunk 1 optimal weight: 6.9990 chunk 25 optimal weight: 10.0000 chunk 40 optimal weight: 5.9990 chunk 23 optimal weight: 20.0000 chunk 29 optimal weight: 0.0970 chunk 27 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 17 optimal weight: 50.0000 overall best weight: 6.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.102196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.084332 restraints weight = 13963.859| |-----------------------------------------------------------------------------| r_work (start): 0.3824 rms_B_bonded: 2.52 r_work: 0.3759 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3696 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3668 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3668 r_free = 0.3668 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1041 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3657 r_free = 0.3657 target_work(ls_wunit_k1) = 0.073 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1058 | |-----------------------------------------------------------------------------| r_final: 0.3657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.5977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 3673 Z= 0.177 Angle : 0.602 11.388 5008 Z= 0.296 Chirality : 0.045 0.134 569 Planarity : 0.005 0.059 613 Dihedral : 6.677 54.326 564 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 0.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.69 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.39), residues: 440 helix: 1.14 (0.53), residues: 97 sheet: 0.45 (0.53), residues: 99 loop : -0.58 (0.37), residues: 244 =============================================================================== Job complete usr+sys time: 1656.00 seconds wall clock time: 29 minutes 59.44 seconds (1799.44 seconds total)